The Bourbon Reforms sought to reduce the power of the church in colonial affairs, a move that was driven by the crown's desire to consolidate its authority and curtail what was seen as the excessive autonomy of the church. The reforms limited the church's ability to accumulate land, regulated ecclesiastical courts, and restricted the jurisdiction of religious orders. This was achieved through the regalist policies that asserted the supremacy of the king over church matters in the colonies. The crown's greater control over clerical appointments and the redirection of church revenues to royal coffers were significant aspects of this strategy.

The Bourbon Reforms addressed colonial defence through a series of military overhauls. They reorganised the colonial militias into a more formal, professional army modelled after European standards. The reforms introduced regiments of professional, paid soldiers and improved fortifications, particularly in strategic locations like Havana and Cartagena, which were vital to the defence against European rivals and pirates. This shift towards a standing military force in the colonies not only enhanced the defensive capabilities of the Spanish empire in the New World but also helped to cement Spanish authority in the colonies by providing a means to enforce the crown's will internally.

In both Spanish and Portuguese colonies, the Jesuits played an influential role in the evangelisation of indigenous peoples, the establishment of educational institutions, and the development of missions that became significant economic enterprises. However, they were profoundly affected by the reforms; the Jesuits were seen as too powerful and autonomous, and their allegiance to the Pope made them suspect in the eyes of the Bourbon monarchs. The Pombaline Reforms particularly targeted them, leading to the expulsion of the Jesuits from Portuguese territories in 1759, while the Bourbon Reforms later saw their expulsion from Spanish territories in 1767. Their properties were seized, and their missions were secularised, which had a substantial impact on the mission economies and the education system.

The Bourbon Reforms profoundly restructured the administrative divisions within Spanish colonies. The introduction of intendancies, a French administrative system, significantly centralised authority. This replaced the older, more fragmented system of corregimientos, thereby diminishing the power of local officials who had often been deeply entrenched in the local elite. Intendants, appointed by the crown, oversaw larger territories than their predecessors and were responsible for tax collection, law enforcement, and public works, which effectively reduced the autonomy of colonial municipalities and increased the direct influence of the Spanish crown over colonial affairs.

In the long term, the Pombaline Reforms laid the foundation for the diversification of the Brazilian economy beyond gold and sugar. They encouraged the production of other commodities, which became important exports, such as rice, cotton, and indigo. The reforms also created a more favourable environment for the growth of domestic industries. However, while they initially boosted the colonial economy and increased royal revenues, these reforms also placed a greater burden on the local population through increased taxes and strict economic controls. The monopolistic practices instituted, particularly those of the Brazil Company, were ultimately detrimental to local businesses and restricted economic growth.